No worrisome coronavirus strains found in Lithuania, but a different one was detected

In mid-December, a new strain of the virus (lineage B.1.1.7 or Variant of Concern, VOC) was detected in the UK. This strain of the virus has been found to compete with other dominant strains and to become one of the most common in the English region. It is believed to have caused a sharp increase in the number of cases.

“Doctors from the Santara Clinics analyzed the positive results of more than 4,000 viral tests carried out in the Santara Clinics laboratory in the Lithuanian population and selected 8 samples in which a loss of signal of the S gene was observed, probably indicating strain B. 1.1.7. To confirm whether a new “worrying” strain has already been detected in Lithuania, it was decided to sequence the genome of these samples. The samples were obtained from the Biobank of Clínicas Santara ”, says Daniel Naumov, Senior Medical Biologist, Head of the Biobank of Clínicas Santara.

For greater precision, sequencing was performed at two centers: UAB Thermo Fisher Scientific Baltics and Santara Clinics Center for Hematology, Oncology and Transfusion The samples were prepared and sequenced by Dr. Justinas Šlikas, senior researcher at Thermo Fisher Scientific Rimvydas Norvilas, biologist doctor of the Center, and Ingrida Olendraitė, researcher in viral molecular biology and bioinformatics at the University of Cambridge, carried out the bioinformatic analysis of the data obtained using the reagents of Thermo Fisher Scientific Baltics of the UAB. The company provided these reagents and performed some of the sequencing for free.

Examination of the SARS-CoV-2 virus strains revealed no “concerns”. B.1.1.7. A strain of B.1.258, which has not been detected in Lithuania by sequencing, was found in all samples and is associated with the United Kingdom, Denmark and Switzerland. Strain B.1.258 found in Lithuania and B.1.1.7 found in the UK have a common mutation: the loss of 69-70 amino acids from protein S, which is believed to be due to an outbreak associated with cultured tissues on farms.

According to the head of the Center for Hematology, Oncology and Transfusionology of Clínicas Santara prof. Laimonas Griškevičius, managed to purposely select samples, perform good quality sequencing, and accurately analyze the data. Viral mutations can affect the accuracy of diagnostic kits, transmission of the virus (infectivity), and the efficacy of the vaccine over time. Currently, the SARS-CoV-2 genomes detected in Lithuania (~ 230; November-December) were found to be easier and therefore more rapidly spreading in VAR (or B.1.1.7) or in the Santara Clinic nor in Lithuanian colleagues analyzed at Vilnius University and Lithuanian University of Health Sciences. did not find. However, at present, with a very high number of infections, these single viral genome studies are insufficient, so it is important to start regular virus sequencing in Lithuania as soon as possible.

On variety B.1.258

The B.1.258 strain is one of the three known strains of the virus in which the S gene signal is lost in routine viral PCR assays. This is associated with the loss of 69-70 amino acids from protein S and is most commonly found in at least three different strains of the strain genome (B.1.1 (hence B.1.1.7), B.1.258 and “group 5”). Also in this strain B.1.258, a mutation in N439K (amino acid of asparagine substituted with lysine) is detected in protein S, which is believed to contribute to the stronger binding of protein S to the human ACE2 receptor.

About the variety B.1.1.7

The strain B.1.1.7 in question has an unusually high number of mutations (17), 8 of which occurred in the S gene responsible for binding to the human cell. This strain was first detected in the UK in September 2020. To date, the same virus has been detected in 29 countries. Preliminary epidemiological studies indicate that strain B.1.1.7 is associated with increased infectivity. This year there is no evidence that this strain affects the severity of the disease or the effectiveness of vaccines.

The importance of sequencing for public health

Theoretically, emerging strains of the virus could have the ability to spread more rapidly in society, leading to milder or more severe forms of the disease. The varieties can also be more difficult to detect in diagnostic tests. Strains should be monitored for possible drug and vaccine resistance.

About SARS-CoV-2 sequencing studies in Lithuania and around the world

In Lithuania, virus sequencing is performed by the Santara Clinics, Vilnius University and the Lithuanian University of Health Sciences. This year, 228 virus genomes have been identified that spread in Lithuania. Unfortunately, such a small number of sequences provides little information on the epidemiological prevalence of virus strains. Epidemiological sequencing studies are applied more widely in the world than in Lithuania. More than 322 thousand sequences of the viral genome have already been uploaded to the international database. The leading country is the United Kingdom, where researchers carry out around 10% of virus sequencing. in all approved cases.